--- Log opened Thu Dec 22 00:00:45 2016
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05:29 < Reventlov> Is there a paperbot there ?
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07:24 < kanzure> Reventlov: paperbot is hibernating for a few hundred years, for now
07:25 < cluckj> RIP paperbot
07:26 < __mz_o> paper will be obsolete by the time he comes out of hibernation
07:28 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=e09eb118 Bryan Bishop: add sha256 hash for original dan boneh video file >> http://diyhpl.us/diyhpluswiki/transcripts/simons-institute/pairing-cryptography/
07:29 < cluckj> everything will be OA by the time paperbot returns
07:30 < kanzure> academia has a tremendous amount of inertia, i'm not sure much is going to change unless someone has a really really good idea
07:30 < kanzure> all the scientists tied up their careers and reputation and work in those journals
07:31 < kanzure> turns out the science people have just as nearly many "consensus problems" as the bitcoin community does
07:31 < cluckj> yes
07:31 < cluckj> it's happening, but very slowly
07:31 < kanzure> i get a little twitchy when people point to scientists as having figured out consensus; no, behind the scenes, academia is a fucking slaughter.
07:32 < cluckj> me too, I wasn't suggesting that :P
07:33 < kanzure> i think that experimental failure in science would be much more tolerable to everyone if the failures were highly interesting (e.g., if this fails, then it will lend tremendous credibility to some other hypothesis)
07:33 < cluckj> the big cultural anthropology went open-access due mostly to my advisors
07:33 < kanzure> unfortunately most of the stuff that fails is boring and "you didn't set it up right" or "it has extremely complex setup requirements and we don't know how to make this not suck so much"
07:34 < cluckj> err big cultural anthropology journal
07:34 < kanzure> (and then reputation gets tied to "look at me! i can unicycle on the head of a pen tip!")
07:34 < kanzure> ((submitted to the proceedings of natural nature, 423nd edition))
07:36 < kanzure> really the reputation should be more tied to capability to reduce complex insane setups into highly repeatable very simple techniques, rather than earning reputation for increasing the spaghetti mess
07:38 < cluckj> maybe
07:38 < kanzure> and then career progression gets to be about increasing the scope of techniques, rather than increasing the scope of various politics and infighting about complexity and "science stunts"
07:39 < cluckj> yeah that sounds like a good idea
07:39 < cluckj> it changes the systemic motivations...
07:40 < cluckj> I think a change in the funding structure would help too (lots of research is done for $$$, so failures are like a thousand variations of "we tried X and it didn't work")
07:40 < cluckj> so failure is totally uninteresting and routinized
07:42 < kanzure> the only kinds of failure that should be allowed are the kinds that provide highly relevant information; if it's just providing 1 or 2 bits of data, it's probably not worthwhile.  in general people should probably be targeting experiments where "failure" reveals 10-20 bits of data.
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07:47 < cluckj> I guess that would require an overhaul of experimental design, and training new scientists to think about experimentation differently
07:47 < cluckj> like having failure modes in hypotheses
07:48 < cluckj> iirc I suggested you read some hans-jorg rheinberger a while ago, did you ever take a look? :P
07:49 < cluckj> he talks about differentiating between the "experimental" (makes new knowledge) and the "testing" (reproduces/proves old knowledge)
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07:55 < kanzure> sorry, didn't you know i'm illiterate?
07:55 < kanzure> "and training new scientists to think about experimentation differently" dunno what you mean. it seems like the only way to think about experimentation, as far as i can tell.
07:57 < cluckj> functionally illiterate :P
07:57 < cluckj> what seems to be the only way to think about experimentation?
07:58 < kanzure> hypotheses, failure modes, the thing where you don't do things until you are sure you're not wasting time
07:58 < cluckj> yeah
07:59 < cluckj> there's particular methods to those that scientists are trained to do
08:00 < cluckj> which do upkeep on the badness in experimental practice
08:03 < cluckj> and the structure of contemporary science (publish-or-perish, promotions for # of papers, etc.) rewards garbage
08:06 < kanzure> nmz787: do you know of a microfluidics structure for cell culturing? for example, a droplet system that encapsulates cells, then a sorting system of some kind where some cells get discarded, and then the ones you keep get to go into a culturing chamber (without the bubble/droplet). have you seen something like this anywhere?
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08:30 < kanzure> "Cell encapsulation via microtechnologies" https://www.researchgate.net/profile/Jisoo_Park2/publication/259805845_Cell_encapsulation_via_microtechnologies/links/0046352fad67c9dd1b000000.pdf
08:33 < kanzure> i guess bubble joining would be called "microfluidic mixing"
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09:05 < Reventlov> kanzure: well, ok
09:06 < Reventlov> (did you see the founder of scihub was nominated by Nature's 10?
09:06 < Reventlov> ( http://www.nature.com/news/nature-s-10-1.21157 )
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10:43 < cluckj> oh boy, a whole rash of citizen science books are coming out
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11:11 < nmz787> kanzure: I've seen all the components of the microfluidic system you ask for... not sure I've seen one that specifically does what you ask, but I've definitely seen all the components unconnected in one paper or another
11:12 < chris_99> cluckj, i'm kind of curious, got any names
11:13 < nmz787> Reventlov: what is paperbot needed for with sci-hub, these days?
11:13 < kanzure> that's not helpful. i'm gonna continue to assume it's called "mixing".
11:14 < cluckj> chris_99, my copy of "citizen science" by caren cooper just got here
11:14 < cluckj> I'll put together more when I'm less busy...
11:14 < chris_99> cheers
11:15 < cluckj> I've only flipped through the intro, but it's reading like a valorization/hagiography of citizen science projects
11:16 < cluckj> (which isn't necessarily a bad thing)
11:16 < kanzure> it's probably easier to do that than to do other kinds of work
11:16 < cluckj> yeah it is
11:16 < cluckj> it's why I don't have a book or several articles out already :P
11:20 < kanzure> nmz787: t-junction.
11:23 < kanzure> hm no.
11:26 < kanzure> "Pillar-induced droplet merging in microfluidic circuits" http://pubs.rsc.org/en/content/articlelanding/2008/lc/b813325e
11:27 < kanzure> "A fast and efficient microfluidic system for highly selective one-to-one droplet fusion" http://pubs.rsc.org/en/content/articlelanding/2009/lc/b903608c
11:32 < nmz787> kanzure: you're trying to find the right word for droplet joiner?
11:32 < nmz787> yeah fusion sounds good
12:06 < kanzure> there's probably an anti-surfactant liquid...
12:09 < kanzure> aha,
12:09 < kanzure> "An electro-coalescence chip for effective emulsion breaking in droplet microfluidics" http://pubs.rsc.org/is/content/articlelanding/2014/lc/c4lc00365a
12:09 < kanzure> "Droplet-based microfluidics is increasingly used for biological applications, where the recovery of cells or particles after an experiment or assay is desirable. Here, we present an electro-demulsification chip which circumvents the use of harsh chemicals and multiple washing/centrifugation steps and offers a mild way for extracting cells and polymer particles into an aqueous phase from micro...
12:10 < kanzure> ...fluidic water-in-oil emulsions."
12:10 < kanzure> this is useful because you can pull cells out of a droplet for their growth/multiply phase
12:11 < kanzure> and then another outlet on the culturing chamber to put cells back into a droplet for individual testing
12:14 < nmz787> but why use a droplet at all if you have that much control?
12:14 < kanzure> well, imagine a homologous recombination evolution setup
12:15 < kanzure> during growth phase, you want them to expand to fill as much volume as they like
12:16 < kanzure> during homologous recombination testing, you want to isolate a cell from all the other cells, introduce dna fragments, give it time to cook, and then analyze the results later, without decoupling the individual cell (genotype) from its recombination results
12:16 < kanzure> underperforming cells should be routed to waste, and high performing cells should be added back into the culture
12:17 < nmz787> sure, but how does a droplet help this?
12:17 < kanzure> the droplet isolates the cell from other cells
12:19 < nmz787> hmm, so I guess the assumption is that would be easier/cheaper than just fabbing apartments for each cell. Seems reasonable if the device wasn't reusable
12:20 < kanzure> the other assumption is that cell color isn't sufficient signal for sorting cells, i guess i forgot to mention that part
12:23 < nmz787> yeah, unless your experiment is somehow connected to a color change... spectroscopy is a sort of color signal though too
12:26 < kanzure> huh? yes you can insert color changes using homologous recombination.
12:27 < nmz787> maybe I should just skip valves for now, and just try to use a syringe to inject the fluid through the fluidic... as a first pass at using the whole system end-to-end (CAD to FAB)
12:29 < nmz787> either that, or I should attempt to model ALL the different valve types into a single test-chip... and see which works best... but that sounds like about 10X more work than I have immediate time for :/
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16:19 < nmz787> kanzure: "Last but not least, it is possible to route the passage of fluids even without valves (at some cost). It is worth noting that the first demonstration of valving in a PDMS device was done in 1999 using...bubbles! Isao Endo's group from RIKEN in Saitama (Japan) used dedicated microchannels to inject air into the fluid-carrying channel so as to obstruct the passage of fluids on demand [59]
16:19 < nmz787> --an approach that is now considered ...
16:19 < nmz787> ... impractical, since the "bubble" is much more stable when it is covered by a PDMS membrane."
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16:19 < kanzure> yes that is the quake-style cross-over channel stuff.   i wouldn't trust it.
16:19 < kanzure> *yes that is otherwise the
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16:42 < nmz787> nah the crossover stuff is mentioned in its own section
16:42 < nmz787> trust is another question though
16:43 < nmz787> I just mentioned it because bubbles
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20:43 < kanzure> bloooop
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21:46 < justanotheruser> are these nanopore sequencers any good
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21:58 < yashgaroth> iirc accuracy is terrible, especially on repetitive stretches; okay for pathogen detection and some other uses
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--- Log closed Fri Dec 23 00:00:46 2016